title: Elucidating functional context within microarray data by integrated transcription factor-focused gene-interaction and regulatory network analysis.
abstract: Microarrays do not yield direct evidence for functional connections between genes. However, transcription factors (TFs) and their binding sites (TFBSs) in promoters are important for inducing and coordinating changes in RNA levels, and thus represent the first layer of functional interaction. Similar to genes, TFs act only in context, which is why a TF/TFBS-based promoter analysis of genes needs to be done in the form of gene(TF)-gene networks, not individual TFs or TFBSs. In addition, integration of the literature and various databases (e.g. GO, MeSH, etc) allows the adding of genes relevant for the functional context of the data even if they were initially missed by the microarray as their RNA levels did not change significantly. Here, we outline a TF-TFBSs network-based strategy to assess the involvement of transcription factors in agonist signaling and demonstrate its utility in deciphering the response of human microvascular endothelial cells (HMEC-1) to leukemia inhibitory factor (LIF). Our strategy identified a central core of eight TFs, of which only STAT3 had previously been definitively linked to LIF in endothelial cells. We also found potential molecular mechanisms of gene regulation in HMEC-1 upon stimulation with LIF that allow for the prediction of changes of genes not used in the analysis. Our approach, which is readily applicable to a wide variety of expression microarray and next generation sequencing RNA-seq results, illustrates the power of a TF-gene networking approach for elucidation of the underlying biology.
authors.affiliation: Genomatix Software GmbH, Munich, Germany. wernersbc@me.com
authors.forename: Thomas
authors.initials: T
authors.lastname: Werner
authors.forename: Susan M
authors.initials: SM
authors.lastname: Dombrowski
authors.forename: Carlos
authors.initials: C
authors.lastname: Zgheib
authors.forename: Fouad A
authors.initials: FA
authors.lastname: Zouein
authors.forename: Henry L
authors.initials: HL
authors.lastname: Keen
authors.forename: Mazen
authors.initials: M
authors.lastname: Kurdi
authors.forename: George W
authors.initials: GW
authors.lastname: Booz
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D042783:Endothelial Cells / Q000378:metabolism*; D015870:Gene Expression; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053605:Leukemia Inhibitory Factor / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012313:RNA / Q000235:genetics; D050796:STAT3 Transcription Factor / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D053605:Leukemia Inhibitory Factor; D050796:STAT3 Transcription Factor; C494086:STAT3 protein, human; D014157:Transcription Factors; D012313:RNA
keywords: high-throughput (HT) approaches; microarray data analysis; transcription factor binding sites; transcription factor-gene networking; transcription factors